Single-photon light detection and ranging (lidar) offers single-photon sensitivity and picosecond timing resolution, which is desirable for high-precision three-dimensional (3D) imaging over long distances. Despite important progress, further extending the imaging range presents enormous challenges because only a few echo photons return and are mixed with strong noise. Here, we tackled these challenges by constructing a high-efficiency, low-noise coaxial single-photon lidar system and developing a long-range-tailored computational algorithm that provides high photon efficiency and good noise tolerance. Using this technique, we experimentally demonstrated active single-photon 3D imaging at a distance of up to 45 km in an urban environment, with a low return-signal level of ～1 photon per pixel. Our system is feasible for imaging at a few hundreds of kilometers by refining the setup, and thus represents a step towards low-power and high-resolution lidar over extra-long ranges.